MolNFT v1 · #113044 · protein
Structure of CEA1A in complex with N-acetylglucosamine
5A3L: “Structure of CEA1A in complex with N-acetylglucosamine”. X-ray diffraction, 4 ligands (NAG, NDG, NA), 9 pockets (best druggability 0.63). MolNFT v1 #113044 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5A3L
- Type
- protein
- Length
- 821 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CEA1
- Ligands
- NAG, NDG, NA, CA
- Pockets
- 9 · best druggability 0.63
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | CEA1 | protein | 209 | 7% helix, 46% strand | — |
| C | CEA1 | protein | 201 | 7% helix, 50% strand | — |
| D | CEA1 | protein | 202 | 6% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B, C, D
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · 5 copies · chains A, C, D
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, B, D
- GOL · Glycerol · additive · 3 copies · chains B, C, D
- CIT · Citric acid · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 268 | 0.63 | 0.81 | 32 | empty |
| 2 | 216 | 0.57 | 0.79 | 32 | empty |
| 3 | 210 | 0.49 | 0.75 | 36 | empty |
| 4 | 219 | 0.49 | 0.75 | 36 | PEG |
| 5 | 84 | 0.42 | 0.79 | 13 | empty |
Interfaces
4 interfaces between chains.
- B–D · 903 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 880 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 228 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 198 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 5A3L · Structure of Cea1A in complex with N-Acetylglucosamine · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 5A3L · PDBe 5A3L
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